How to name files, the sequel

Transcript

1. How to Name Files
   Like a Normie
   pos.it/how-to-name-
   fi
   les
   Jenny Bryan
   
   Posit, PBC
   
   t
   @JennyBryan
   
   g
   @jennybc
   
   m
   @[email protected]
   

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2. Check out Jason Bourne, 6 minutes in!
   

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3. Pick a filename convention
   Any convention
   Just pick one
   

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4. myabstract.docx
   
   
   Jane’s Filenames Use “Spaces” & Punctuation ;).xlsx
   
   
   figure 1.png
   
   
   JW7d^(2sl@deletethisandyourcareerisoverWx2*.txt
   2022-09-24_abstract-for-normconf.docx
   
   
   janes-filenames-are-getting-better.xlsx
   
   
   fig01_scatterplot-talk-length-vs-interest.png
   
   
   1986-01-28_raw-data-from-challenger-o-rings.txt
   YES
   NO
   

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5. good file names are ...
   • machine readable
   • human readable
   • sorted in a useful way
   

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6. > ls
   
   
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A01.csv
   
   
   ...
   
   
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_H02.csv
   
   
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_H03.csv
   
   
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_platefile.csv
   
   
   2014-02-26_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41_A01.csv
   
   
   2014-02-26_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41_A02.csv
   
   
   2014-02-26_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41_A03.csv
   
   
   ...
   
   
   > ls *Plasmid*
   
   
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A01.csv
   
   
   ...
   
   
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_H02.csv
   
   
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_H03.csv
   
   
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_platefile.csv
   globbing
   

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7. tibble(filenames) |>
   
   
   separate_wider_delim(
   
   
   filenames,
   
   
   delim = regex("[_\\.]"),
   
   
   names = c("date", "assay", "line", "well", NA)
   
   
   )
   
   
   #> # A tibble: 25 × 4
   
   
   #> date assay line well
   
   
   #>
   
   
   #> 1 2013-06-26 BRAFWTNEGASSAY Plasmid-Cellline-100-1MutantFraction A01
   
   
   #> 2 2013-06-26 BRAFWTNEGASSAY Plasmid-Cellline-100-1MutantFraction A02
   
   
   #> 3 2013-06-26 BRAFWTNEGASSAY Plasmid-Cellline-100-1MutantFraction A03
   
   
   ...
   2014-02-26_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41_A03.csv
   _ Underscore to delimit
   fi
   elds
   
   - Hyphen to delimit words within
   fi
   elds
   regular expressions
   

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8. Thou shalt get only as
   creative with names as
   thine own skill with
   regular expressions.
   

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9. machine readable
   • regular expression and globbing friendly
   
   - avoid spaces, punctuation, accented characters, case sensitivity
   
   • easy to compute on
   
   - deliberate use of delimiters
   

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10. 01.md
    
    
    01.R
    
    
    02.md
    
    
    02.R
    
    
    03.md
    
    
    03.R
    
    
    04.md
    
    
    04.R
    
    
    9.md
    
    
    90.R
    
    
    figure/
    
    
    helpers.R
    
    
    Makefile
    01_marshal-data.md
    
    
    01_marshal-data.R
    
    
    02_pre-dea-filtering.md
    
    
    02_pre-dea-filtering.R
    
    
    03_dea-with-limma-voom.md
    
    
    03_dea-with-limma-voom.R
    
    
    04_explore-dea-results.md
    
    
    04_explore-dea-results.R
    
    
    90_limma-model-term-name-fiasco.md
    
    
    90_limma-model-term-name-fiasco.R
    
    
    figure/
    
    
    helper01_load-counts.R
    
    
    helper02_load-exp-des.R
    
    
    helper03_load-focus-statinf.R
    
    
    helper04_extract-and-tidy.R
    
    
    Makefile
    

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11. embrace the slug
    01_marshal-data.R
    
    
    02_pre-dea-filtering.R
    
    
    03_dea-with-limma-voom.R
    
    
    04_explore-dea-results.R
    

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12. human readable
    • make it easy to guess what the heck something is,
    based on its name
    

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13. 01_marshal-data.R
    
    
    02_pre-dea-filtering.R
    
    
    03_dea-with-limma-voom.R
    
    
    04_explore-dea-results.R
    
    
    90_limma-model-term-name-fiasco.R
    
    
    figure/
    
    
    helper01_load-counts.R
    
    
    helper02_load-exp-des.R
    
    
    helper03_load-focus-statinf.R
    
    
    helper04_extract-and-tidy.R
    
    
    Makefile
    2015-11-09_package-installation.R
    
    
    2015-12-23_package-installation.R
    
    
    2016-05-21_package-installation.R
    
    
    2016-07-30_package-installation.R
    
    
    2017-09-05_package-installation.R
    
    
    2018-06-29_package-installation.R
    
    
    2019-02-19_repair-default-library.R
    
    
    2019-06-25_package-installation.R
    
    
    2020-06-06_record-existing-pkgs.R
    
    
    2021-06-15_git-config-analysis.R
    
    
    2021-07-19_fix-https-git-urls.R
    
    
    2021-08-29_git-default-branch-analysis.R
    
    
    2022-08-11_rebuilding-my-user-library.R
    
    
    2022-08-11_record-existing-pkgs.R
    chronological
    logical
    

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14. 10_final-figs-for-publication.R
    
    
    1_data-cleaning.R
    
    
    2_fit-model.R
    
    
    ...
    01_data-cleaning.R
    
    
    02_fit-model.R
    
    
    ...
    
    
    10_final-figs-for-publication.R
    YES
    NO
    

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15. Comprehensive
    map of all countries
    in the world that
    use MM-DD-YYYY
    https://twitter.com/donohoe/status/597876118688026624
    

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16. ISO 8601
    for the love of god, please
    2022-12-15
    

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17. sorted in a useful way
    •plan for alphanumeric sorting
    
    •put something numeric-ish
    fi
    rst-ish
    
    •use the ISO 8601 standard for dates
    
    •left pad numbers with zeros
    

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18. good file names are ...
    • machine readable
    • human readable
    • sorted in a useful way
    pos.it/how-to-name-
    fi
    les
    
    t
    @JennyBryan
    
    g
    @jennybc
    
    m
    @[email protected]
    

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